Modeling and Computational Chemistry References


Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F., and Weng, J. (1987) Protein Data Bank, in Crystallographic Databases - Information Content, Software Systems, Scientific Applications (F. H. Allen, G. Bergerhoff & R. Sievers, eds.) Data Commission of the International Union of Crystallography, Bonn, pp. 107-132.

Allen, F. H., Bellar, S., Brice, M. D., Cartwright, B. A., doubleday, A., Higgs, H. Hummelink, T., Hummeling-Peters, B. G., Kennard, O., Motherwell, M. D. S., Rodgers, J. R., & Watson, D. G., (1979) The Cambridge Crystallographic Datra Centre: Computer-Based Search, Retrieval, Analysis and Display of Information, Acta Cryst. B35, 2331-2339.

Allinger, N. L. (1977) Conformational Analysis 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms, J. Am. Chem. Soc. 99, 8127-8134.

Allinger, N. L., Kok, R. A., and Imam, M. R. (1988) Hydrogen Bonding in MM2, J. Comp. Chem. 9, 591-595.

Allinger, N. L., Yuh, Y. H., & Lii, J-H. (1989) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1. J. Am. Chem. Soc. 111, 8551-8565.

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tamusi, M. (1977) The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures, J. Mol. Biol. 112, 535-542.

Besler, B. H., Merz, K. M., & Kollman, P. A. (1990) Atomic Charges Derived from Semiempirical Methods, J. Comp. Chem. 11, 431-439 (1990).

Bol, J. E., Buning, C., Comba, P., Reedijk, J. and Strohle, M. (1998) Molecular mechanics modeling of organic backbone of metal-free and coordinated ligands, J. Comp. Chem. 19, 512-523

Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations. J. Comp. Chem. (1983) 4, 187-217.

Burkert, U., & Allinger, N. L. (1982) Molecular Mechanics, American Chemical Society, Washington, DC.

Clark, M., Cramer III, R. D., van Opdenhosch, N., (1989) Validation of the General Purpose Tripose 5.2 Force Field, J. Comp. Chem. 10, 982-1012.

Comba, P., and Hambley, T. W. (1995) Molecular Modeling of Inorganic Compounds, VCH, Weinheim, Germany.

Dupuis, M., Spangler, D., & Wendoloski, J. J., (1980) Program QC01, National Resource for Computations in Chemistry Software Catalog, University of California, Berkeley, CA.

Dupuis, M., Watts, J. D., Villar, H. O., & Hurst, G. J. B., (1989a) The General Atomic and Molecular Electronic Structrue System: HONDO 7.0, Comput. Phys. Comm. 52, 415-425.

Dupuis, M., Mougenot, P., Watts, J. D., Hurst, G. J. B., & Villar, H. O.,(1989b) HONDO: A General Atomic and Molecular Electronic Structure System, in MOTECC: Modern Techniques in Computational Chemistry (E. Clementi, Ed.) ESCOM, Leiden, the Netherlands, pp. 306-361.

 Frisch, M. G., Trucks, G. W., Head-Gordon, M., Gill, P. M. W., Wong, M. W., Foresman, J. B., Johnson, B. G., Schlegel, H. B., Robb, M. A., Replogle, E. S., Gomperts, R., Andres, J. L., Raghavachari, K., Binkley, j. S., Gonzalez, C., Martin, R. L., Fox, D. J., Defrees, D. J., Baker, J., Stewart, J. J. P., & Pople, J. A., (1992) Gaussian 92, Gaussian Inc., Pittsburgh, PA.

Gibson, K. D., & Scheraga, H. A., (1986) Proc. natl. Acad. Sci. USA 83, 5649-5653.

Hay, B. P. (1993) Methods for molecular mechanics modeling of coordination compounds, Coord. Chem. Rev. 126, 177-236.

Hay, B. P., Yang, L., Lii, J-H., and Allinger, N. L. (1998) An extended MM3(96) force field for complexes of the group 1A and 2A cations with ligands bearing conjugated ether donor groups, Theochem: J. Molecular Structure 428, 203-219,

Hermans, J., Berendsen, H. J. C., van Gunsteren, W. F., & Postma, J. P. M., (1984) A Consistent Empirical Potential for Water-Protein Interactions, Biopolymers 23, 1513-1518.

Jorgensen, W. L., & Tirado-Rives, J.,(1988) The OPLS Potential Functions for Proteins. Energy Minimization for Crystals of Cyclic Peptides and Crambin, J. Am. Chem. Soc. 110, 1657-1666.

Krippahl, L. (1996) "BoGIE - Boolian Geometric Interaction Evaluation," Graduation's thesis, Universidade Nova de Lisboa, Portugal.

Lii, J-H., Gallion,S., Bender,C., Wikstrom, H., Allinger, N. L., Flurchick, K. M., and Teeter, M. M.,(1989) Molecular Mechanics (MM2) Calculations on Peptides and on the Protein Crambin Using the Cyber 205, J. Comp. Chem. 10, 503-513.

Lii, J-H., & Allinger, N. L. (1989a) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2. Vibrational Frequencies and Thermodynamics, J. Am. Chem. Soc. 111, 8566-8575.

Lii, J-H., & Allinger, N. L. (1989b) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 3. The van der Waals' Potentials and Crystal data for Aliphatic and Aromatic Hydrocarbons, J. Am. Chem. Soc. 111, 8576-8582.

Lii, J-H., & Allinger, N. L. (1991) The MM3 Force Field for Amides, Polypeptides and Proteins, J. Comp. Chem. 12, 186-199.

Lii, J-H., & Allinger, N. L. (1998) Directional Hydrogen Bonding in the MM3 Force Field. II. J. Comp. Chem. 19, 1001-1016.

Mohamadi, F., Richards, N. G. J., Guida, W. C., Liskamp, R., Lipton, M., Caufield, C., Chang, G., Hendrickson, T., and Still, W. C., (1990) MacroModel- An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics, J. Comp. Chem. 11, 440-467.

Momany, F. A., McGuire, R. F., Burgess, A. W., & Scheraga, H. A., (1975) Energy Parameters in Polypeptides VII, Geometric Parameters, Partial Charges, Non-bonded Interactions, Hydrogen Bond Interactions and Intrensic Torsional Potentials for Naturally Ocurring Amino Acids, J. Phys. Chem. 79, 2361-2381.

Momany, F. A., & Rone, R., (1992) Validation of the General Purpose QUANTA 3.2/CHARMm Force Field, J. Comp. Chem. 13, 888-900.

Mulholland, A. J., Grand, G. H. and Richards, W. G., "Computer Modeling of Enzyme Catalysed Reaction Mechanisms" Protein Engineering 6, 113-147 (1993).

Nemethy, G., Pottle, M. S., & Scheraga, H. A., (1983) Energy Paramters in Polypeptides, 9. Updating of Geometrical Parameters, Non-bonding Interactions and Hydrogen Bonding INteractions for Naturally Occuring Amino Acids, J. PHys. Chem. 87, 1883-1887.

Northrup, S. H.,& Erickson, H. P. (1992) "Kinetics of protein protein association explained by brownian dynamics computer- simulation," PNAS (USA) 89, 3338-3342.

Pearlman, D. A., Case, D. A., Caldwell, J. C., Seibel, G. L., Singh, U. C., Weiner, P., & Kollman, P. A., (1991) AMBER 4.0, University of California, San Francisco.

Saenger, W. (1984) Principles of nucleic acid Structure., Springer-verlag, NY. (1984)

Salahub, D. R., and Zerner, M. C. (1989) The Challenge of d and f electrons, American Chemical Society, Washington, D. C.

Sippl, M. J., Nemethy, G., & Scheraga, H. A., (1984) Intermolecular Potentials for Crystal Data 6. Determination of Empirical Potentials for 0-H---O=C Hydrogen Bonds for Packing Configurations, J. Phys. Chem. 88, 6231-6633.

Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Jensen, J. H., Koseki, S., Gordon, M. S., Nguyen, K. A., Windus, T. L., & Gordon, M. S., (1990) QCPE Bulletin 10, 52-54.

Spellmeyer, D.C., Swope, W. C., & Evensen, E. R., (1989) San Francisco Package of Applications for the Simulation of Molecular Systems, Regents of the University of California, San Francisco, CA.

Stewart, J. J. P., (1990) J. Computer-Aided Mol. Des. 4, 1-105.

Stewart, D. E., & Wampler, J. E. (1991) "Molecular Dynamics Simulations of the Cytochrome c3-Rubredoxin Complex" Proteins 11, 142-152.

van Gunsteren, W. F., Berendsen, H. J. C., Hermans, J., Hole, W. G. J., & Postma, J. P. M. (1983) Computer Simulation of the Dynamics of Hydrated Protein Crystals and Its Comparison with X-ray Data, Proc. Natl. Acad. Sci. USA, 80, 4315-4319.

Vedani, A., Dobler, M., Dunitz, J.D. An empirical potential function for metal centers: Application to molecular mechanics calculations on metalloproteins. J. Comp. Chem. (1986) 7, 701-710.

Vedani, A.: YETI: An interactive molecular mechanics program for small-molecule protein complexes. J. Comp. Chem. (1988) 9, 269-280.

Vedani, A., and Huhta, D. W.: A New Force Field for Modeling Metalloproteins. J. Am. Chem. Soc. (1990) 112, 4759-4767.

Wampler, J. E. (1994) Computational Chemistry and Molecular Modeling of Electron Transfer Proteins, IN Methods in Enzymology (Peck, H. D., Jr., LeGall, J., Eds) Academic Press, New York, pp. 559-607.

Weiner, P. K., & Kollman, P. A., (1981) AMBER: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions, J. Comp. Chem. 2, 287-303.

Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., Jr., Weiner, P.K. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.

Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., (1986) "An All Atom Force Field for Simulations of Proteins and Nucleic Acids," J. Comp. Chem. 7, 230-252.

 


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